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617b339d0e
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617b339d0e | ||
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a51a1284f2 |
@ -16,47 +16,53 @@ public:
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~PBLane();
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private:
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//泳道过滤处理函数
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//根据输入所有类似泳道的中心X轴坐标（groupsX），以及泳道的最小最大距离（minDifference/maxDifference），过滤掉不合规的泳道
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std::vector<int> processArray(std::vector<int>& groupsX, int minDifference, int maxDifference);
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//宽度/*流*/计算函数，用来计算检测泳道宽度流
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vector<int> get_bar_num(vector<unsigned char> buf);
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//泳道检测补全函数
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//根据泳道位置（processX）和泳道间距离（meanW），从图像（src）中检测临近类泳道位置是否符合泳道特性（泳道内两条像素的宽度流应类似且存在条带）
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std::vector<int> checkArray(std::vector<int>& processX, Mat src, int start_y, int end_y, int meanW);
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//条带信息计算函数，输入8bit数组（rbuf）以及过滤范围（range）（此范围内仅保留一个分子）
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vector<std::array<int, 3>> get_top_point(vector<unsigned char> rbuf, int range);
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//单个泳道中条带信息计算（条带位置等）
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BandInfo get_protein_lane_data(Mat src, Rect lane);
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static bool myCompare(const int& a, const int& b);
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static bool myCompare2(const std::array<int, 4>& a, const std::array<int, 4>& b);
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public:
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//函数：获得图像中泳道位置
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//src：输入图像，需是8bit单通道图像
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//返回值：泳道矩形位置信息
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std::vector<cv::Rect> getProteinRect(Mat src);
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// std::vector<cv::Rect> getProteinRect(Mat src);
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//获得蛋白泳道位置，src是灰度图像CV_8UC1，*ProteinRect_width 是蛋白泳道宽度（keep_width = 1时，输入固定宽度；keep_width = 0时,输出计算得到宽度），
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//ProteinRect_height_ratio高度比例，高度占图像高度百分之几，一般输入90
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//返回所有蛋白泳道矩形
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std::vector<cv::Rect> getProteinRect(Mat src,int* ProteinRect_width,bool keep_width,int ProteinRect_height_ratio);
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//添加泳道，proteinRect是当前泳道矩形，x是新添加泳道的中心x坐标，一般就是鼠标点击图形的x坐标,
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//src是输入图形（CV_16UC1）,unadjustbands是未对齐条带信息，需要同步修改
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void addProteinRect(std::vector<cv::Rect>& proteinRect,int x,Mat src,std::vector<BandInfo>& unadjustbands);
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//删除泳道，proteinRect是当前泳道矩形，idx是删除泳道的下标序号,unadjustbands是未对齐条带信息，需要同步修改
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void deleteProteinRect(std::vector<cv::Rect>& proteinRect,int idx,std::vector<BandInfo>& unadjustbands);
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//计算单个泳道条带信息，src是输入图形（CV_16UC1），lane是泳道对应矩形，
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//返回BandInfo条带结果
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BandInfo get_protein_lane_data(Mat src,Rect lane);
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//获得所有泳道未对齐的条带结果，src是输入图形（CV_16UC1），lane是泳道对应矩形
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//返回所有泳道未对齐的条带结果
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std::vector<BandInfo> getProteinBands(Mat src,std::vector<cv::Rect> lanes);
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//修改泳道宽度和高度和已经计算出的未对齐条带信息，src是输入图形（CV_16UC1），proteinRect是当前泳道矩形，
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//ProteinRect_width是新的蛋白泳道宽度,ProteinRect_height_ratio是新的高度比例，高度占图像高度百分之几，一般输入90
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//unadjustbands是未对齐的所有泳道条带信息
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//输入的条带必须是未对齐的，调整后数据需要重新对齐和计算分子量（调用adjustBands和molecularWeightResult）
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void modifyProteinRectAndBands(Mat src,std::vector<cv::Rect>& proteinRect,int ProteinRect_width,int ProteinRect_height_ratio,std::vector<BandInfo>& unadjustbands);
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//根据鼠标点击图形的坐标，输出当前位置的泳道下标和条带下标
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//lanes是泳道信息，bands是对应条带信息（不关心对齐或者未对齐），x、y是坐标，lanesIndex是传回鼠标点击位置的泳道下标，bandsIndex是鼠标点击位置的条带下标
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void getLaneBandsIndex(std::vector<cv::Rect> lanes,std::vector<BandInfo> bands,int x,int y,int* lanesIndex,int* bandsIndex);
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//根据鼠标点击图形的坐标添加条带,lanes是泳道信息，lanesIndex是鼠标点击位置是第几条泳道，unadjustbands是未对齐的所有泳道条带信息，原始鼠标点击位置的y坐标
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//输入的条带必须是未对齐的，调整后数据需要重新对齐和计算分子量（调用adjustBands和molecularWeightResult）
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void addProteinBand(std::vector<cv::Rect> lanes,int lanesIndex,std::vector<BandInfo>& unadjustbands,int y);
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//根据鼠标点击图形的坐标删除条带,lanesIndex是鼠标点击位置是第几条泳道，unadjustbands是未对齐的所有泳道条带信息，bandsIndex是鼠标点击位置是第几个条带
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//输入的条带必须是未对齐的，调整后数据需要重新对齐和计算分子量（调用adjustBands和molecularWeightResult）
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void deleteProteinBand(int lanesIndex,std::vector<BandInfo>& unadjustbands,int bandsIndex);
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//对齐所有泳道的条带结果，unadjustbands是所有泳道的条带结果，range是条带中心在多少像素范围内属于同一类型条带，一般写10
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//返回对齐后的所有泳道的条带结果（未计算分子量）
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std::vector<BandInfo> adjustBands(std::vector<BandInfo> unadjustbands, int range);
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//计算得到分子量结果
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void molecularWeightResult(std::vector<cv::Rect> lanes,std::vector<BandInfo>& bands);
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////函数：获得图像中泳道对应的条带信息
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////src：输入图像，需是16bit单通道图像
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////lanes：泳道矩形位置信息
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////返回值：对应条带位置信息
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std::vector<BandInfo> getProteinBands(Mat src, std::vector<cv::Rect> lanes);
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////函数：条带分子匹配排序函数
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////bands：所有条带位置信息
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////range：Y轴差在range范围内的表示和泳道1匹配
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////返回值：结果修改在bands中
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void adjustBands(std::vector<BandInfo>& bands, int range);
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////函数：计算所有条带的分子信息
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////lanes：输入泳道信息
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////bands：输入条带信息，对应输出的分子信息在这个结构体中
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void molecularWeightResult(std::vector<cv::Rect> lanes, std::vector<BandInfo>& bands);
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};
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@ -259,7 +259,7 @@ std::vector<int> PBLane::checkArray(std::vector<int>& processX, Mat src, int sta
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return result;
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}
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vector<std::array<int, 3>> PBLane::get_top_point(vector<unsigned char> rbuf, int range)
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vector<std::array<int, 3>> PBLane::get_top_point(vector<unsigned short> rbuf, int range)
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{
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vector<std::array<int, 2>> point;
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vector<char> diff(rbuf.size());
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@ -279,7 +279,7 @@ vector<std::array<int, 3>> PBLane::get_top_point(vector<unsigned char> rbuf, int
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}
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for (int i = rbuf.size() - 1; i >= 0; i--)
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{
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if (diff[i] == 0 && i == rbuf.size() - 1)
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if (i == rbuf.size() - 1 && diff[i] == 0)
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{
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diff[i] = 1;
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}
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@ -437,37 +437,12 @@ vector<std::array<int, 3>> PBLane::get_top_point(vector<unsigned char> rbuf, int
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return topPoint;
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}
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BandInfo PBLane::get_protein_lane_data(Mat src, Rect lane)
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{
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BandInfo band;
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int sum = 0;
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vector<unsigned char> cdata;
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for (int i = lane.y; i < lane.y + lane.height; i++)
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{
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sum = 0;
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for (int j = lane.x; j < lane.x + lane.width; j++)
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{
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sum += src.at<unsigned short>(i, j);
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}
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sum /= lane.width;
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band.land_data.push_back((unsigned short)sum);
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band.ydata.push_back((float)((65535 - sum) / 255.0));
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cdata.push_back((unsigned char)((65535 - sum) >> 8));
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}
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for (int i = 0; i < lane.height; i++)
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{
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band.xdata.push_back((float)i / lane.height);
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}
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band.band_point = get_top_point(cdata, 8);
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return band;
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}
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PBLane::PBLane() {}
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PBLane::~PBLane() {}
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std::vector<cv::Rect> PBLane::getProteinRect(Mat src)
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std::vector<cv::Rect> PBLane::getProteinRect(Mat src,int* ProteinRect_width,bool keep_width,int ProteinRect_height_ratio)
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{
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cv::Mat edges;
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Canny(src, edges, 50, 150);
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@ -483,7 +458,7 @@ std::vector<cv::Rect> PBLane::getProteinRect(Mat src)
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continue;
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}
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double rotia = 0.0;
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rotia = (double)rect.width / rect.height;
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rotia = (double)rect.width/rect.height;
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if (rotia >= 7 || rotia <= 2) {
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continue;
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}
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@ -495,27 +470,28 @@ std::vector<cv::Rect> PBLane::getProteinRect(Mat src)
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std::vector<int> allW(boundingRects.size());
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int up = src.rows;
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int down = 0;
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for (int i = 0; i < boundingRects.size(); i++)
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for (int i = 0;i<boundingRects.size();i++)
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{
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allX[i] = boundingRects[i].x + boundingRects[i].width / 2;
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allY[i] = boundingRects[i].y + boundingRects[i].height / 2;
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allX[i] = boundingRects[i].x + boundingRects[i].width/2;
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allY[i] = boundingRects[i].y + boundingRects[i].height/2;
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allW[i] = boundingRects[i].width;
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up = min(boundingRects[i].y, up);
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down = max(boundingRects[i].y + boundingRects[i].height, down);
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up = min(boundingRects[i].y,up);
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down = max(boundingRects[i].y + boundingRects[i].height,down);
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}
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int meanW = 0;
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int meanY = 0;
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int maxH = 0;
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std::sort(allW.begin(), allW.end(), myCompare);
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std::sort(allY.begin(), allY.end(), myCompare);
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std::sort(allX.begin(), allX.end(), myCompare);
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std::sort(allW.begin(), allW.end(), [](const int& a, const int& b) {
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return a < b;
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});
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std::sort(allY.begin(), allY.end(), [](const int& a, const int& b) {
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return a < b;
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});
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std::sort(allX.begin(), allX.end(), [](const int& a, const int& b) {
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return a < b;
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});
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int cnt = 0;
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if (boundingRects.size() == 0)
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{
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std::vector<cv::Rect> proteinRect1(boundingRects.size());
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return proteinRect1;
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}
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for (int i = boundingRects.size() / 3; i <= 2 * boundingRects.size() / 3; i++)
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for(int i = boundingRects.size()/3;i <= 2*boundingRects.size()/3;i++)
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{
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cnt++;
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meanW += allW[i];
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@ -524,37 +500,99 @@ std::vector<cv::Rect> PBLane::getProteinRect(Mat src)
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meanW /= cnt;
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meanY /= cnt;
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maxH = max(down - meanY, meanY - up) * 2;
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maxH = max(maxH, src.rows / 3);
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maxH = max(maxH,src.rows/3);
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std::vector<int> groupsX;
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const int n = 3;
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int sumX = allX[0];
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cnt = 1;
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for (int i = 1; i < boundingRects.size(); i++) {
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if (allX[i] - allX[i - 1] > n)
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if (allX[i] - allX[i-1] > n)
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{
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groupsX.push_back(sumX / cnt);
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groupsX.push_back(sumX/cnt);
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sumX = 0;
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cnt = 0;
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}
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sumX += allX[i];
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cnt++;
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}
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groupsX.push_back(sumX / cnt);
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groupsX.push_back(sumX/cnt);
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std::vector<int> processX = processArray(groupsX, meanW, meanW * 1.8);
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std::vector<int> proteinX = checkArray(processX, src, 15, src.rows - 30, meanW);
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std::vector<int> processX = processArray(groupsX,meanW,meanW*1.8);
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std::vector<int> proteinX = checkArray(processX, src,15,src.rows - 30,meanW);
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std::vector<cv::Rect> proteinRect(proteinX.size());
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for (int i = 0; i < proteinX.size(); i++)
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for(int i = 0;i<proteinX.size();i++)
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{
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proteinRect[i].x = proteinX[i] - meanW / 2;
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proteinRect[i].y = 15;//meanY - maxH/2;
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if(keep_width == 1){
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meanW = *ProteinRect_width;
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}
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else{
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*ProteinRect_width = meanW;
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}
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int y_start = src.rows * (100 - ProteinRect_height_ratio) / 200;
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proteinRect[i].x = proteinX[i] - meanW/2;
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proteinRect[i].y = y_start;
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proteinRect[i].width = meanW;
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proteinRect[i].height = src.rows - 30;
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proteinRect[i].height = src.rows - y_start * 2;
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}
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return proteinRect;
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}
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void PBLane::addProteinRect(std::vector<cv::Rect>& proteinRect,int x,Mat src,std::vector<BandInfo>& unadjustbands)
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{
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Rect new_proteinRect;
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new_proteinRect.x = x - proteinRect[0].width/2;
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new_proteinRect.y = proteinRect[0].y;
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new_proteinRect.width = proteinRect[0].width;
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new_proteinRect.height = proteinRect[0].height;
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BandInfo band = get_protein_lane_data(src,new_proteinRect);
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for (auto it = proteinRect.begin(); it != proteinRect.end(); ++it) {
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if (it->x > new_proteinRect.x) {
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size_t index = std::distance(proteinRect.begin(), it);
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proteinRect.insert(it, new_proteinRect);
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unadjustbands.insert(unadjustbands.begin() + index, band);
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return;
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}
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}
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proteinRect.push_back(new_proteinRect);
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unadjustbands.push_back(band);
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return;
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}
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void PBLane::deleteProteinRect(std::vector<cv::Rect>& proteinRect,int idx,std::vector<BandInfo>& unadjustbands)
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{
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if (idx < proteinRect.size()) {
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proteinRect.erase(proteinRect.begin() + idx);
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unadjustbands.erase(unadjustbands.begin() + idx);
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} else {
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std::cout << "idx out of range!" << std::endl;
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}
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return;
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}
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BandInfo PBLane::get_protein_lane_data(Mat src, Rect lane)
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{
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BandInfo band;
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int sum = 0;
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vector<unsigned short> cdata;
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for (int i = lane.y; i < lane.y + lane.height; i++)
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{
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sum = 0;
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for (int j = lane.x; j < lane.x + lane.width; j++)
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{
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sum += src.at<unsigned short>(i, j);
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}
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sum /= lane.width;
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band.land_data.push_back((unsigned short)sum);
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band.ydata.push_back((float)((65535 - sum) / 255.0));
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cdata.push_back(65535 - sum);
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}
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for (int i = 0; i < lane.height; i++)
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{
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band.xdata.push_back((float)i / lane.height);
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}
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band.band_point = get_top_point(cdata, 8);
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return band;
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}
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std::vector<BandInfo> PBLane::getProteinBands(Mat src, std::vector<cv::Rect> lanes)
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{
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@ -580,11 +618,198 @@ std::vector<BandInfo> PBLane::getProteinBands(Mat src, std::vector<cv::Rect> lan
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return bands;
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}
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void PBLane::adjustBands(std::vector<BandInfo>& bands, int range)
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void PBLane::modifyProteinRectAndBands(Mat src,std::vector<cv::Rect>& proteinRect,int ProteinRect_width,int ProteinRect_height_ratio,std::vector<BandInfo>& unadjustbands)
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{
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// 用于存储所有的值及其对应的列索引
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int y_start = src.rows * (100 - ProteinRect_height_ratio) / 200;
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int det_y = proteinRect[0].y - y_start;
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for(int i = 0;i<proteinRect.size();i++)
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{
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proteinRect[i].x = proteinRect[i].x - (ProteinRect_width - proteinRect[i].width)/2;
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proteinRect[i].y = y_start;
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proteinRect[i].width = ProteinRect_width;
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proteinRect[i].height = src.rows - y_start * 2;
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}
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int sum = 0;
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for(int n = 0; n < proteinRect.size(); n++)
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{
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unadjustbands[n].land_data.clear();
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unadjustbands[n].ydata.clear();
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unadjustbands[n].xdata.clear();
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for(int i = proteinRect[n].y; i < proteinRect[n].y + proteinRect[n].height; i++)
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{
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sum = 0;
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for(int j = proteinRect[n].x; j < proteinRect[n].x + proteinRect[n].width; j++)
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{
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sum+=src.at<unsigned short>(i,j);
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}
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sum/=proteinRect[n].width;
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unadjustbands[n].land_data.push_back((unsigned short)sum);
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unadjustbands[n].ydata.push_back((float)((65535 - sum)/255.0));
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}
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for(int i = 0; i < proteinRect[n].height; i++)
|
||||
{
|
||||
unadjustbands[n].xdata.push_back((float)i/proteinRect[n].height);
|
||||
}
|
||||
|
||||
for(int i = 0; i < unadjustbands[n].band_point.size(); i++)
|
||||
{
|
||||
//fix left and right
|
||||
unadjustbands[n].band_point[i][1] += det_y;
|
||||
unadjustbands[n].band_point[i][2] += det_y;
|
||||
//fix top
|
||||
int y1 = unadjustbands[n].band_point[i][1];
|
||||
int y2 = unadjustbands[n].band_point[i][2];
|
||||
float temp = unadjustbands[n].ydata[y1];
|
||||
for(int j = y1 + 1; j < y2; j++)
|
||||
{
|
||||
if(unadjustbands[n].ydata[j] > temp){
|
||||
temp = unadjustbands[n].ydata[j];
|
||||
unadjustbands[n].band_point[i][0] = j;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void PBLane::getLaneBandsIndex(std::vector<cv::Rect> lanes,std::vector<BandInfo> bands,int x,int y,int* lanesIndex,int* bandsIndex)
|
||||
{
|
||||
*lanesIndex = -1;
|
||||
*bandsIndex = -1;
|
||||
int ystart = lanes[0].y;
|
||||
int yend = lanes[0].y + lanes[0].height - 1;
|
||||
if(y > yend || y < ystart)
|
||||
{
|
||||
return ;
|
||||
}
|
||||
for (int i = 0; i < lanes.size(); i++) {
|
||||
int xstart = lanes[i].x;
|
||||
int xend = lanes[i].x + lanes[i].width - 1;
|
||||
if(x <= xend && x >= xstart){
|
||||
*lanesIndex = i;
|
||||
break;
|
||||
}
|
||||
}
|
||||
for (int j = 0; j < bands[*lanesIndex].band_point.size(); j++) {
|
||||
int y1 = bands[*lanesIndex].band_point[j][1] + ystart;
|
||||
int y2 = bands[*lanesIndex].band_point[j][2] + ystart;
|
||||
if(y <= y2 && y >= y1){
|
||||
*bandsIndex = j;
|
||||
break;
|
||||
}
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
void PBLane::addProteinBand(std::vector<cv::Rect> lanes,int lanesIndex,std::vector<BandInfo>& unadjustbands,int y)
|
||||
{
|
||||
int ystart = lanes[lanesIndex].y;
|
||||
int yend = lanes[lanesIndex].y + lanes[lanesIndex].height - 1;
|
||||
int y1 = 0;
|
||||
int y2 = lanes[lanesIndex].height;
|
||||
if(y < ystart || y > yend)
|
||||
{
|
||||
return ;
|
||||
}
|
||||
int rect_y = y - lanes[lanesIndex].y;
|
||||
for(int i = 0; i < unadjustbands[lanesIndex].band_point.size(); i++)
|
||||
{
|
||||
y2 = unadjustbands[lanesIndex].band_point[i][1];
|
||||
if(rect_y >= y1 && rect_y < y2)
|
||||
{
|
||||
break;
|
||||
}
|
||||
else
|
||||
{
|
||||
y1 = unadjustbands[lanesIndex].band_point[i][2];
|
||||
}
|
||||
|
||||
}
|
||||
if(y1 > y2)
|
||||
{
|
||||
y2 = lanes[lanesIndex].height;
|
||||
}
|
||||
|
||||
//fine top
|
||||
int range = 8;
|
||||
int top_start = rect_y - range;
|
||||
int top_end = rect_y + range;
|
||||
if(top_start < y1){
|
||||
top_start = y1;
|
||||
}
|
||||
if(top_end > y2){
|
||||
top_end = y2;
|
||||
}
|
||||
std::array<int, 3> new_band_point;
|
||||
new_band_point[0] = top_start;
|
||||
float temp = unadjustbands[lanesIndex].ydata[top_start];
|
||||
float mean = unadjustbands[lanesIndex].ydata[top_start];
|
||||
for(int i = top_start + 1; i < top_end; i++)
|
||||
{
|
||||
mean += unadjustbands[lanesIndex].ydata[i];
|
||||
if(unadjustbands[lanesIndex].ydata[i] > temp){
|
||||
temp = unadjustbands[lanesIndex].ydata[i];
|
||||
new_band_point[0] = i;
|
||||
}
|
||||
}
|
||||
mean /= (top_end - top_start);
|
||||
|
||||
//fine left
|
||||
temp = unadjustbands[lanesIndex].ydata[new_band_point[0]];
|
||||
new_band_point[1] = y1;
|
||||
for(int i = new_band_point[0] - 1; i > y1; i--)
|
||||
{
|
||||
if(unadjustbands[lanesIndex].ydata[i] > temp)
|
||||
{
|
||||
if(temp < mean)
|
||||
{
|
||||
new_band_point[1] = i+1;
|
||||
break;
|
||||
}
|
||||
}
|
||||
temp = unadjustbands[lanesIndex].ydata[i];
|
||||
}
|
||||
//fine right
|
||||
temp = unadjustbands[lanesIndex].ydata[new_band_point[0]];
|
||||
new_band_point[2] = y2;
|
||||
for(int i = new_band_point[0] + 1; i < y2; i++)
|
||||
{
|
||||
if(unadjustbands[lanesIndex].ydata[i] > temp)
|
||||
{
|
||||
if(temp < mean)
|
||||
{
|
||||
new_band_point[2] = i+1;
|
||||
break;
|
||||
}
|
||||
}
|
||||
temp = unadjustbands[lanesIndex].ydata[i];
|
||||
}
|
||||
|
||||
for (auto it = unadjustbands[lanesIndex].band_point.begin(); it != unadjustbands[lanesIndex].band_point.end(); ++it) {
|
||||
if ((*it)[0] > new_band_point[0]) {
|
||||
unadjustbands[lanesIndex].band_point.insert(it, new_band_point);
|
||||
return;
|
||||
}
|
||||
}
|
||||
unadjustbands[lanesIndex].band_point.push_back(new_band_point);
|
||||
return ;
|
||||
}
|
||||
|
||||
void PBLane::deleteProteinBand(int lanesIndex,std::vector<BandInfo>& unadjustbands,int bandsIndex)
|
||||
{
|
||||
if (bandsIndex < unadjustbands[lanesIndex].band_point.size()) {
|
||||
unadjustbands[lanesIndex].band_point.erase(unadjustbands[lanesIndex].band_point.begin() + bandsIndex);
|
||||
} else {
|
||||
std::cout << "bandsIndex out of range!" << std::endl;
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
|
||||
std::vector<BandInfo> PBLane::adjustBands(std::vector<BandInfo> unadjustbands, int range)
|
||||
{
|
||||
// 用于存储所有的值及其对应的列索引
|
||||
std::map<int, int> columnMap;
|
||||
std::vector<BandInfo> bands = unadjustbands;
|
||||
|
||||
std::vector<std::array<int, 4>> vec;
|
||||
for (int i = 0; i < bands.size(); i++)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user